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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 10-89439022-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=89439022&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 89439022,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000371790.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC16A12",
"gene_hgnc_id": 23094,
"hgvs_c": "c.610C>T",
"hgvs_p": "p.Arg204Trp",
"transcript": "NM_213606.4",
"protein_id": "NP_998771.3",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 516,
"cds_start": 610,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 949,
"cdna_end": null,
"cdna_length": 4655,
"mane_select": "ENST00000371790.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC16A12",
"gene_hgnc_id": 23094,
"hgvs_c": "c.610C>T",
"hgvs_p": "p.Arg204Trp",
"transcript": "ENST00000371790.5",
"protein_id": "ENSP00000360855.4",
"transcript_support_level": 2,
"aa_start": 204,
"aa_end": null,
"aa_length": 516,
"cds_start": 610,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 949,
"cdna_end": null,
"cdna_length": 4655,
"mane_select": "NM_213606.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC16A12",
"gene_hgnc_id": 23094,
"hgvs_c": "c.610C>T",
"hgvs_p": "p.Arg204Trp",
"transcript": "XM_017016237.3",
"protein_id": "XP_016871726.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 516,
"cds_start": 610,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 947,
"cdna_end": null,
"cdna_length": 4653,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC16A12",
"gene_hgnc_id": 23094,
"hgvs_c": "c.610C>T",
"hgvs_p": "p.Arg204Trp",
"transcript": "XM_017016238.2",
"protein_id": "XP_016871727.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 516,
"cds_start": 610,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 950,
"cdna_end": null,
"cdna_length": 4656,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC16A12",
"gene_hgnc_id": 23094,
"hgvs_c": "c.610C>T",
"hgvs_p": "p.Arg204Trp",
"transcript": "XM_017016239.2",
"protein_id": "XP_016871728.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 516,
"cds_start": 610,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 809,
"cdna_end": null,
"cdna_length": 4515,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC16A12",
"gene_hgnc_id": 23094,
"hgvs_c": "c.610C>T",
"hgvs_p": "p.Arg204Trp",
"transcript": "XM_047425221.1",
"protein_id": "XP_047281177.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 516,
"cds_start": 610,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 937,
"cdna_end": null,
"cdna_length": 4643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC16A12",
"gene_hgnc_id": 23094,
"hgvs_c": "c.610C>T",
"hgvs_p": "p.Arg204Trp",
"transcript": "XM_047425222.1",
"protein_id": "XP_047281178.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 516,
"cds_start": 610,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 944,
"cdna_end": null,
"cdna_length": 4650,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC16A12",
"gene_hgnc_id": 23094,
"hgvs_c": "c.610C>T",
"hgvs_p": "p.Arg204Trp",
"transcript": "XM_047425223.1",
"protein_id": "XP_047281179.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 516,
"cds_start": 610,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 853,
"cdna_end": null,
"cdna_length": 4559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC16A12-AS1",
"gene_hgnc_id": 51205,
"hgvs_c": "n.99+6808G>A",
"hgvs_p": null,
"transcript": "ENST00000765073.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 392,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC16A12",
"gene_hgnc_id": 23094,
"dbsnp": "rs758404955",
"frequency_reference_population": 0.00001672964,
"hom_count_reference_population": 0,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.0000171025,
"gnomad_genomes_af": 0.0000131467,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9106210470199585,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.49000000953674316,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.634,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3932,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.13,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.274,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.49,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000371790.5",
"gene_symbol": "SLC16A12",
"hgnc_id": 23094,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AD",
"hgvs_c": "c.610C>T",
"hgvs_p": "p.Arg204Trp"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000765073.1",
"gene_symbol": "SLC16A12-AS1",
"hgnc_id": 51205,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.99+6808G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Developmental cataract,Juvenile cataract-microcornea-renal glucosuria syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Developmental cataract|Juvenile cataract-microcornea-renal glucosuria syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}